@article{Aqvist1994,
abstract = {A new semi-empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.},
author = {{\AA}qvist, J and Medina, C and Samuelsson, J E},
issn = {0269-2139},
journal = {Protein engineering},
month = {mar},
number = {3},
pages = {385--91},
pmid = {8177887},
title = {{A new method for predicting binding affinity in computer-aided drug design.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8177887},
volume = {7},
year = {1994}
}
@article{Aqvist1991,
author = {{\AA}qvist, Johan},
doi = {10.1021/j100165a002},
issn = {0022-3654},
journal = {The Journal of Physical Chemistry},
month = {jun},
number = {12},
pages = {4587--4590},
title = {{Free energy perturbation study of metal ion-catalyzed proton transfer in water}},
url = {http://pubs.acs.org/doi/abs/10.1021/j100165a002},
volume = {95},
year = {1991}
}
@article{Aqvist1993,
author = {{\AA}qvist, Johan and Warshel, Arieh},
doi = {10.1021/cr00023a010},
issn = {0009-2665},
journal = {Chemical Reviews},
month = {nov},
number = {7},
pages = {2523--2544},
title = {{Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches}},
url = {http://pubs.acs.org/doi/10.1021/cr00023a010},
volume = {93},
year = {1993}
}
@book{berendsenintermolecular,
author = {Berendsen, H J C and Postma, J P M and van Gunsteren, W F and Hermans, J},
editor = {Pullman, B.},
pages = {331--342},
publisher = {Reidel: Dordrecht, The Netherlands},
title = {{Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981}},
year = {1981}
}
@article{Berendsen1984,
author = {Berendsen, H. J. C. and Postma, J. P. M. and van Gunsteren, W. F. and DiNola, A. and Haak, J. R.},
doi = {10.1063/1.448118},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
month = {oct},
number = {8},
pages = {3684--3690},
title = {{Molecular dynamics with coupling to an external bath}},
url = {http://aip.scitation.org/doi/10.1063/1.448118},
volume = {81},
year = {1984}
}
@article{Berkowitz1982,
author = {Berkowitz, Max and McCammon, J. Andrew},
doi = {10.1016/0009-2614(82)80028-6},
issn = {00092614},
journal = {Chemical Physics Letters},
month = {jul},
number = {3},
pages = {215--217},
title = {{Molecular dynamics with stochastic boundary conditions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0009261482800286},
volume = {90},
year = {1982}
}
@article{Beveridge1989,
author = {Beveridge, D L and DiCapua, F M},
doi = {10.1146/annurev.bb.18.060189.002243},
issn = {0883-9182},
journal = {Annual Review of Biophysics and Biophysical Chemistry},
month = {jun},
number = {1},
pages = {431--492},
title = {{Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bb.18.060189.002243},
volume = {18},
year = {1989}
}
@article{Brooks1983,
author = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D. and States, David J. and Swaminathan, S. and Karplus, Martin},
doi = {10.1002/jcc.540040211},
issn = {0192-8651},
journal = {Journal of Computational Chemistry},
number = {2},
pages = {187--217},
title = {{CHARMM: A program for macromolecular energy, minimization, and dynamics calculations}},
url = {http://doi.wiley.com/10.1002/jcc.540040211},
volume = {4},
year = {1983}
}
@article{Brunger1984,
author = {Br{\"{u}}nger, Axel and Brooks, Charles L. and Karplus, Martin},
doi = {10.1016/0009-2614(84)80098-6},
issn = {00092614},
journal = {Chemical Physics Letters},
month = {mar},
number = {5},
pages = {495--500},
title = {{Stochastic boundary conditions for molecular dynamics simulations of ST2 water}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0009261484800986},
volume = {105},
year = {1984}
}
@article{Ceperley1995,
author = {Ceperley, D. M.},
doi = {10.1103/RevModPhys.67.279},
issn = {0034-6861},
journal = {Reviews of Modern Physics},
month = {apr},
number = {2},
pages = {279--355},
title = {{Path integrals in the theory of condensed helium}},
url = {https://link.aps.org/doi/10.1103/RevModPhys.67.279},
volume = {67},
year = {1995}
}
@article{Cornell1995,
author = {Cornell, Wendy D. and Cieplak, Piotr and Bayly, Christopher I. and Gould, Ian R. and Merz, Kenneth M. and Ferguson, David M. and Spellmeyer, David C. and Fox, Thomas and Caldwell, James W. and Kollman, Peter A.},
doi = {10.1021/ja00124a002},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
month = {may},
number = {19},
pages = {5179--5197},
title = {{A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja00124a002},
volume = {117},
year = {1995}
}
@article{Eldridge1997,
abstract = {This paper describes the development of a simple empirical scoring function designed to estimate the free energy of binding for a protein-ligand complex when the 3D structure of the complex is known or can be approximated. The function uses simple contact terms to estimate lipophilic and metal-ligand binding contributions, a simple explicit form for hydrogen bonds and a term which penalises flexibility. The coefficients of each term are obtained using a regression based on 82 ligand-receptor complexes for which the binding affinity is known. The function reproduces the binding affinity of the complexes with a cross-validated error of 8.68 kJ/mol. Tests on internal consistency indicate that the coefficients obtained are stable to changes in the composition of the training set. The function is also tested on two test sets containing a further 20 and 10 complexes, respectively. The deficiencies of this type of function are discussed and it is compared to approaches by other workers.},
author = {Eldridge, M D and Murray, C W and Auton, T R and Paolini, G V and Mee, R P},
issn = {0920-654X},
journal = {Journal of computer-aided molecular design},
month = {sep},
number = {5},
pages = {425--45},
pmid = {9385547},
title = {{Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9385547},
volume = {11},
year = {1997}
}
@article{Essex1995,
author = {Essex, Jonathan W. and Jorgensen, William L.},
doi = {10.1002/jcc.540160805},
issn = {0192-8651},
journal = {Journal of Computational Chemistry},
month = {aug},
number = {8},
pages = {951--972},
title = {{An empirical boundary potential for water droplet simulations}},
url = {http://doi.wiley.com/10.1002/jcc.540160805},
volume = {16},
year = {1995}
}
@book{feynman1965quantum,
author = {Feynman, R P and Hibbs, A R},
file = {:home/acmnpv/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Feynman, Hibbs - 1965 - Quantum mechanics and path integrals.pdf:pdf},
publisher = {McGraw-Hill},
series = {International series in pure and applied physics},
title = {{Quantum mechanics and path integrals}},
url = {https://books.google.se/books?id=14ApAQAAMAAJ},
year = {1965}
}
@book{Frenkel:1996,
address = {Orlando, FL, USA},
edition = {1st},
editor = {Frenkel, Daan and Smit, Berend},
isbn = {0122673700},
publisher = {Academic Press, Inc.},
title = {{Understanding Molecular Simulation: From Algorithms to Applications}},
year = {1996}
}
@article{Gao2008,
author = {Gao, Jiali and Wong, Kin-Yiu and Major, Dan T.},
doi = {10.1002/jcc.20810},
file = {:home/acmnpv/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Gao, Wong, Major - 2008 - Combined QMMM and path integral simulations of kinetic isotope effects in the proton transfer reaction between.pdf:pdf},
issn = {01928651},
journal = {Journal of Computational Chemistry},
month = {mar},
number = {4},
pages = {514--522},
title = {{Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water}},
url = {http://doi.wiley.com/10.1002/jcc.20810},
volume = {29},
year = {2008}
}
@book{Gunsteren1996,
abstract = {Computer Applications -- Physical Sciences and Engineering.},
address = {Z{\"{u}}rich; Groningen; Z{\"{u}}rich},
author = {van. Gunsteren, Wilfred F and Billeter, S.R. and Eising, A.A. and H{\"{u}}nenberger, P.H. and Kr{\"{u}}ger, P. and Mark, A.E. and Tironi, I.G.},
isbn = {3728124222 9783728124227},
language = {English},
publisher = {Biomos ; Vdf, Hochschulverlag AG an der ETH Z{\"{u}}rich},
title = {{Biomolecular simulation : the GROMOS96 manual and user guide}},
year = {1996}
}
@article{Hansson1998,
abstract = {A recent method for estimating ligand binding affinities is extended. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. This type of method may be useful for computational prediction of ligand binding strengths, e.g., in drug design applications.},
author = {Hansson, Tomas and Marelius, John and {\AA}qvist, J},
doi = {10.1023/A:1007930623000},
issn = {0920-654X},
journal = {Journal of computer-aided molecular design},
month = {jan},
number = {1},
pages = {27--35},
pmid = {9570087},
title = {{Ligand binding affinity prediction by linear interaction energy methods.}},
url = {http://link.springer.com/10.1023/A:1007930623000 http://www.ncbi.nlm.nih.gov/pubmed/9570087},
volume = {12},
year = {1998}
}
@article{HUMP96,
author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus},
journal = {Journal of Molecular Graphics},
pages = {33--38},
title = {{VMD -- Visual Molecular Dynamics}},
volume = {14},
year = {1996}
}
@article{Hwang1993,
author = {Hwang, Jenn Kang and Warshel, Arieh},
doi = {10.1021/j100141a026},
issn = {0022-3654},
journal = {The Journal of Physical Chemistry},
month = {sep},
number = {39},
pages = {10053--10058},
title = {{A quantized classical path approach for calculations of quantum mechanical rate constants}},
url = {http://pubs.acs.org/doi/abs/10.1021/j100141a026},
volume = {97},
year = {1993}
}
@article{Isaksen2015,
author = {Isaksen, Geir Villy and Andberg, Tor Arne Heim and {\AA}qvist, Johan and Brandsdal, Bj{\o}rn Olav},
doi = {10.1016/j.jmgm.2015.05.007},
issn = {10933263},
journal = {Journal of Molecular Graphics and Modelling},
month = {jul},
pages = {15--23},
title = {{Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1093326315000856},
volume = {60},
year = {2015}
}
@article{Jones-Hertzog1997,
author = {Jones-Hertzog, Deborah K. and Jorgensen, William L.},
doi = {10.1021/jm960684e},
issn = {0022-2623},
journal = {Journal of Medicinal Chemistry},
month = {may},
number = {10},
pages = {1539--1549},
title = {{Binding Affinities for Sulfonamide Inhibitors with Human Thrombin Using Monte Carlo Simulations with a Linear Response Method}},
url = {http://pubs.acs.org/doi/abs/10.1021/jm960684e},
volume = {40},
year = {1997}
}
@article{Jorgensen1983b,
author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
doi = {10.1063/1.445869},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
month = {jul},
number = {2},
pages = {926--935},
title = {{Comparison of simple potential functions for simulating liquid water}},
url = {http://aip.scitation.org/doi/10.1063/1.445869},
volume = {79},
year = {1983}
}
@article{Jorgensen1996a,
author = {Jorgensen, William L. and Maxwell, David S. and Tirado-Rives, Julian},
doi = {10.1021/ja9621760},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
month = {jan},
number = {45},
pages = {11225--11236},
title = {{Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja9621760},
volume = {118},
year = {1996}
}
@article{Jorgensen1988,
author = {Jorgensen, William L. and Tirado-Rives, Julian},
doi = {10.1021/ja00214a001},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
month = {mar},
number = {6},
pages = {1657--1666},
title = {{The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja00214a001},
volume = {110},
year = {1988}
}
@article{Kollman1993,
author = {Kollman, Peter.},
doi = {10.1021/cr00023a004},
issn = {0009-2665},
journal = {Chemical Reviews},
month = {nov},
number = {7},
pages = {2395--2417},
title = {{Free energy calculations: Applications to chemical and biochemical phenomena}},
url = {http://pubs.acs.org/doi/abs/10.1021/cr00023a004},
volume = {93},
year = {1993}
}
@article{Kolmodin1999,
author = {Kolmodin, Karin and {\AA}qvist, Johan},
doi = {10.1016/S0014-5793(99)00974-6},
issn = {00145793},
journal = {FEBS Letters},
month = {aug},
number = {2},
pages = {301--305},
title = {{Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase}},
url = {http://doi.wiley.com/10.1016/S0014-5793{\%}2899{\%}2900974-6},
volume = {456},
year = {1999}
}
@article{Laaksonen1992,
abstract = {The program SCARECROW has been developed to help the molecular modeler to analyze and display the very big and complex data files produced by molecular dynamics programs. The molecular graphics program SCARECROW is written to support the display, animation, and extensive analysis of molecular dynamics trajectories. Using the macro language it is easy to make scripts for video animation and for the automated display and analysis of time series. Extensive coloring and atom selection commands are included to help the user to focus on relevant regions of the molecule. Time series can be produced and viewed on the screen or transferred to other programs.},
author = {Laaksonen, L},
issn = {0263-7855},
journal = {Journal of molecular graphics},
month = {mar},
number = {1},
pages = {33--4, 24},
pmid = {1504051},
title = {{A graphics program for the analysis and display of molecular dynamics trajectories.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1504051},
volume = {10},
year = {1992}
}
@article{Maier2015a,
author = {Maier, James A. and Martinez, Carmenza and Kasavajhala, Koushik and Wickstrom, Lauren and Hauser, Kevin E. and Simmerling, Carlos},
doi = {10.1021/acs.jctc.5b00255},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = {aug},
number = {8},
pages = {3696--3713},
title = {{ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB}},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255},
volume = {11},
year = {2015}
}
@article{Major2007a,
author = {Major, Dan Thomas and Gao, Jiali},
doi = {10.1021/ct600371k},
file = {:home/acmnpv/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Major, Gao - 2007 - An Integrated Path Integral and Free-Energy Perturbation−Umbrella Sampling Method for Computing Kinetic Isotope Ef.pdf:pdf},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = {may},
number = {3},
pages = {949--960},
title = {{An Integrated Path Integral and Free-Energy Perturbation−Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct600371k},
volume = {3},
year = {2007}
}
@article{Marelius1998,
abstract = {A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-binding selectivity and free energy profiles for nucleophile activation in two protein tyrosine phosphatases as well as absolute binding affinity estimation for a lysine-binding protein are given as examples.},
author = {Marelius, John and Kolmodin, Karin and Feierberg, Isabella and {\AA}qvist, Johan},
doi = {10.1016/S1093-3263(98)80006-5},
issn = {10933263},
journal = {Journal of Molecular Graphics and Modelling},
month = {aug},
number = {4-6},
pages = {213--225},
title = {{Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems}},
url = {http://www.sciencedirect.com/science/article/pii/S1093326399000121 http://linkinghub.elsevier.com/retrieve/pii/S1093326399000121},
volume = {16},
year = {1998}
}
@article{Martyna1992,
author = {Martyna, Glenn J. and Klein, Michael L. and Tuckerman, Mark},
doi = {10.1063/1.463940},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
month = {aug},
number = {4},
pages = {2635--2643},
title = {{Nos{\'{e}}–Hoover chains: The canonical ensemble via continuous dynamics}},
url = {http://aip.scitation.org/doi/10.1063/1.463940},
volume = {97},
year = {1992}
}
@article{Muegge1999,
author = {Muegge, Ingo and Martin, Yvonne C.},
doi = {10.1021/jm980536j},
issn = {0022-2623},
journal = {Journal of Medicinal Chemistry},
month = {mar},
number = {5},
pages = {791--804},
title = {{A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach}},
url = {http://pubs.acs.org/doi/abs/10.1021/jm980536j},
volume = {42},
year = {1999}
}
@misc{qtools,
author = {Purg, Miha and Bauer, Paul},
doi = {10.5281/zenodo.842003},
month = {aug},
title = {qtools v0.5.9},
url = {https://doi.org/10.5281/zenodo.842003},
year = {2017}
}
@article{Robertson2015a,
author = {Robertson, Michael J. and Tirado-Rives, Julian and Jorgensen, William L.},
doi = {10.1021/acs.jctc.5b00356},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = {jul},
number = {7},
pages = {3499--3509},
title = {{Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field}},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00356},
volume = {11},
year = {2015}
}
@article{Schneider1978,
author = {Schneider, T. and Stoll, E.},
doi = {10.1103/PhysRevB.17.1302},
issn = {0163-1829},
journal = {Physical Review B},
month = {feb},
number = {3},
pages = {1302--1322},
title = {{Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions}},
url = {https://link.aps.org/doi/10.1103/PhysRevB.17.1302},
volume = {17},
year = {1978}
}
@misc{gunsteren:87,
author = {van Gunsteren, Wilfred F. and Berendsen},
howpublished = {Biomos, Nijenborgh 16, Groningen, NL},
keywords = {bibtex-import},
title = {{Groningen Molecular Simulation (GROMOS) Library Manual}},
year = {1987}
}
@article{Wang2002,
abstract = {New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions. All three scoring functions are calibrated through multivariate regression analysis of a set of 200 protein-ligand complexes and they reproduce the binding free energies of the entire training set with standard deviations of 2.2 kcal/mol, 2.1 kcal/mol, and 2.0 kcal/mol, respectively. These three scoring functions are further combined into a consensus scoring function, X-CSCORE. When tested on an independent set of 30 protein-ligand complexes. X-CSCORE is able to predict their binding free energies with a standard deviation of 2.2 kcal/mol. The potential application of X-CSCORE to molecular docking is also investigated. Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking.},
author = {Wang, Renxiao and Lai, Luhua and Wang, Shaomeng},
issn = {0920-654X},
journal = {Journal of computer-aided molecular design},
month = {jan},
number = {1},
pages = {11--26},
pmid = {12197663},
title = {{Further development and validation of empirical scoring functions for structure-based binding affinity prediction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12197663},
volume = {16},
year = {2002}
}
@article{Warshel1978a,
author = {Warshel, A.},
doi = {10.1016/0009-2614(78)84013-5},
issn = {00092614},
journal = {Chemical Physics Letters},
month = {may},
number = {3},
pages = {454--458},
title = {{A microscopic model for calculations of chemical processes in aqueous solutions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0009261478840135},
volume = {55},
year = {1978}
}
@article{Warshel2003,
author = {Warshel, Arieh},
doi = {10.1146/annurev.biophys.32.110601.141807},
issn = {1056-8700},
journal = {Annual Review of Biophysics and Biomolecular Structure},
month = {jun},
number = {1},
pages = {425--443},
title = {{Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights}},
url = {http://www.annualreviews.org/doi/10.1146/annurev.biophys.32.110601.141807},
volume = {32},
year = {2003}
}
@book{Warshel1997,
author = {Warshel, Arieh},
edition = {Wiley Prof},
file = {:home/acmnpv/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Warshel - 1997 - Computer Modeling of Chemical Reactions in Enzymes and Solutions.pdf:pdf},
isbn = {0-471-18440-3},
publisher = {Wiley Interscience},
title = {{Computer Modeling of Chemical Reactions in Enzymes and Solutions}},
year = {1997}
}
@article{Zacharias1994,
author = {Zacharias, M. and Straatsma, T. P. and McCammon, J. A.},
doi = {10.1063/1.466707},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
month = {jun},
number = {12},
pages = {9025--9031},
title = {{Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration}},
url = {http://aip.scitation.org/doi/10.1063/1.466707},
volume = {100},
year = {1994}
}
@misc{vmdhomepage,
title = {{http://www.ks.uiuc.edu/Research/vmd/}}
}
@misc{gomhomepage,
title = {http://www.csc.fi/{\~{}}laaksone/gopenmol/gopenmol.html}
}
@misc{pdb,
title = {http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2 frame.html}
}
